rapport: a report templating system in r

rapport: a report templating system in RLiterate programming with global options and local arguments

Gergely Darczi & Aleksandar [email protected]

@daroczig

useR! 2014, Los Angeles, USA

Some custom R packages for reportingR report templates with inputs

1 rapportoolsHelper functions to be used inside of textual reports.

2 panderTurning R objects into markdown.

3 rapport

Gergely Darczi (rapporter.net) rapport: a report templating system in R useR! 2014 2 / 23

What is pander?A collection of helper functions to print markdown syntax

> ?pandoc.(footnote|header|horizontal.rule|image|link|p)(.return)?> ?pandoc.(emphasis|strikeout|strong|verbatim)(.return)?

> pandoc.strong(foobar)**foobar**

> pandoc.strong.return(foobar)[1] "**foobar**"

> pandoc.header(foobar, level = 2)

## foobar

> pandoc.header(foobar, style = setext)

foobar======


What is pander?Collection of helper functions to map R objects to markdown

> ?pandoc.(list|table)(.return)?

> pandoc.list(list(foo, list(bar)))

* foo* bar

> pandoc.table(head(iris, 2), split.table = Inf)

-------------------------------------------------------------------Sepal.Length Sepal.Width Petal.Length Petal.Width Species

-------------- ------------- -------------- ------------- ---------5.1 3.5 1.4 0.2 setosa

4.9 3 1.4 0.2 setosa-------------------------------------------------------------------


What is pander?Collection of helper functions to map R objects to various markdown languages

> pandoc.table(head(iris, 2), split.table = Inf, style = rmarkdown)

| Sepal.Length | Sepal.Width | Petal.Length | Petal.Width | Species ||:--------------:|:-------------:|:--------------:|:-------------:|:---------:|| 5.1 | 3.5 | 1.4 | 0.2 | setosa || 4.9 | 3 | 1.4 | 0.2 | setosa |

> pandoc.table(head(iris, 2), split.table = Inf, style = simple)

Sepal.Length Sepal.Width Petal.Length Petal.Width Species-------------- ------------- -------------- ------------- ---------

5.1 3.5 1.4 0.2 setosa4.9 3 1.4 0.2 setosa


What is pander?Collection of helper functions to map R objects to various markdown languages

> iris$Species

What is pander?S3 method to map R objects to markdown

> ?pander(.return)?

> methods(pander)

[1] pander.anova* pander.aov* pander.cast_df* pander.character*

[5] pander.data.frame* pander.default* pander.density* pander.evals*

[9] pander.factor* pander.glm* pander.htest* pander.image*

[13] pander.list* pander.lm* pander.logical* pander.matrix*

[17] pander.NULL* pander.numeric* pander.option pander.POSIXct*

[21] pander.POSIXt* pander.prcomp* pander.rapport* pander.table*

Non-visible functions are asterisked

> pander(head(iris, 1), split.table = Inf)

-------------------------------------------------------------------

Sepal.Length Sepal.Width Petal.Length Petal.Width Species

-------------- ------------- -------------- ------------- ---------

5.1 3.5 1.4 0.2 setosa

-------------------------------------------------------------------



> pander(letters[1:7])

_a_, _b_, _c_, _d_, _e_, _f_ and _g_

> pander(ks.test(runif(50), runif(50))

---------------------------------------------------

Test statistic P value Alternative hypothesis

---------------- --------- ------------------------

0.18 _0.3959_ two-sided

---------------------------------------------------

Table: Two-sample Kolmogorov-Smirnov test: runif(50) and runif(50)

> pander(chisq.test(table(mtcars$am, mtcars$gear)))

---------------------------------------

Test statistic df P value

---------------- ---- -----------------

20.94 2 _2.831e-05_ * * *

---------------------------------------

Table: Pearsons Chi-squared test: table(mtcars$am, mtcars$gear)

Warning message:In chisq.test(table(mtcars$am, mtcars$gear)) :Chi-squared approximation may be incorrect



> pander(lm(mtcars$wt ~ mtcars$hp), summary = TRUE)

--------------------------------------------------------------

Estimate Std. Error t value Pr(>|t|)

----------------- ---------- ------------ --------- ----------

**mtcars$hp** 0.009401 0.00196 4.796 4.146e-05

**(Intercept)** 1.838 0.3165 5.808 2.389e-06

--------------------------------------------------------------

-------------------------------------------------------------

Observations Residual Std. Error $R^2$ Adjusted $R^2$

-------------- --------------------- ------- ----------------

32 0.7483 0.4339 0.4151

-------------------------------------------------------------

Table: Fitting linear model: mtcars$wt ~ mtcars$hp


What is pander?S3 method to map multiple R objects to markdown

> mtable123 pander(mtable123)

--------------------------------------------------

Model 1 Model 2 Model 3

----------------- ---------- ---------- ----------

**(Intercept)** -1.821 20.556*** 18.875***

(32.325) (0.542) (1.103)

**wt** 46.160*** -0.319

(9.625) (0.328)

**hp** -0.018***

(0.003)

**R-squared** 0.434 0.502 0.031

**F** 22.999 30.190 0.945

**p** 0.000 0.000 0.339

**N** 32 32 32

--------------------------------------------------


What is pander?S3 method to map R objects to pretty formatted markdown

> panderOptions(table.split.table, Inf)

> panderOptions(table.style, grid)

> emphasize.cells(which(iris > 1.3, arr.ind = TRUE))

> pander(iris)

+----------------+---------------+----------------+---------------+------------+

| Sepal.Length | Sepal.Width | Petal.Length | Petal.Width | Species |

+================+===============+================+===============+============+

| *5.1* | *3.5* | *1.4* | 0.2 | setosa |

+----------------+---------------+----------------+---------------+------------+

| *4.9* | *3* | *1.4* | 0.2 | setosa |

+----------------+---------------+----------------+---------------+------------+

| *4.7* | *3.2* | 1.3 | 0.2 | setosa |

+----------------+---------------+----------------+---------------+------------+

| *4.6* | *3.1* | *1.5* | 0.2 | setosa |

+----------------+---------------+----------------+---------------+------------+

| *5* | *3.6* | *1.4* | 0.2 | setosa |

+----------------+---------------+----------------+---------------+------------+

| *5.4* | *3.9* | *1.7* | 0.4 | setosa |

+----------------+---------------+----------------+---------------+------------+

| *4.6* | *3.4* | *1.4* | 0.3 | setosa |

+----------------+---------------+----------------+---------------+------------+

| *5* | *3.4* | *1.5* | 0.2 | setosa |

+----------------+---------------+----------------+---------------+------------+

| *4.4* | *2.9* | *1.4* | 0.2 | setosa |

+----------------+---------------+----------------+---------------+------------+


What does pander do inside of rapport?A tool for literate programming that automatically transforms R objects into markdown

# A quick analyis on mtcars

The mean of is and the standarddeviation is . Let us also check thefrequency table:

## Tables are boring!


What does pander do inside of rapport?Pandoc.brew: markdown results

# A quick analyis on mtcars

The mean of am is _0.4062_ and the standarddeviation is _0.499_. Let us also check thefrequency table:

-------0 1

--- ---19 13-------


![Histogram of am](/tmp/RtmphL0K2Q/plots/f2457fb575.png)

...


What does pander do inside of rapport?Pandoc.brew: calling Pandoc to convert the results to HTML


What does pander do inside of rapport?Pandoc.brew: calling Pandoc to convert the results to MS docx


rapport overviewThe overall structure of a reusable report template

## Subtitle with

http://rapport-package.info/Gergely Darczi (rapporter.net) rapport: a report templating system in R useR! 2014 16 / 23

rapport demoHeader: meta information on the reporting template and input(s) specification


rapport demoBody: normal text with brew-style code chunks

# A quick analyis on

The mean of is and thestandard deviation is . Let us alsocheck the frequency table:



rapport demo

> rapport(rapport-demo, data = mtcars, v = am)

# A quick analyis on _am_

The mean of am is _0.4062_ and thestandard deviation is _0.499_. Let us alsocheck the frequency table:

-------0 1

--- ---19 13-------


![Histogram of am](/tmp/RtmphL0K2Q/plots/f2457fb575.png)


A bit more complex demoAnalysing the results of a dialect survey with Google Maps and ordinary English language

http://blog.rapporter.net/2013/07/uk-dialect-maps.html


Rapporter packagesAll released under AGPL, designed to be deployed in web applications

pander: A Pandocs markdown writer in Rrapport: A report templating system with dynamic inputs

rapportools: Helpers functionssandboxR: Filtering malicious R calls

Further documentation:

http://rapport-package.info/

http://rapporter.github.io/pander/

http://hackme.rapporter.net

http://blog.rapporter.net

Q & A: [email protected]


Why pander?Custom featres

brew loops and conditional parts of a report just like with brew,capturing plots and images with automatically applied theme,render all R objects automatically in Pandocs markdown,recording all warning/error messages plus the raw R objects alongwith anything printed to stdout and the printed results,custom caching mechanism to disk or RAM with auto-dependecy,convert to HTML/pdf/odt/docx at one go,no chunk options (only workaround),building reports also in interactive session with an R5 reference class.

http://rapporter.github.io/pander/#brew-to-pandoc


rapport: a report templating system in r

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